[gmx-users] confusion about pdb file and coordinate.xvg file

Justin Lemkul jalemkul at vt.edu
Mon Feb 4 14:40:39 CET 2013

On 2/4/13 8:06 AM, biki wrote:
> Hi all,
> I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version.
> I have generated the trajectory file using trjconv utility in gromacs. Using the  trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water using g_traj utility. I thought I will get the same value of co-ordinates of H atoms  in both the files in a particular time step. But it was not so. I am attaching here a part of both the files containing the co-ordinates of H atoms in the first time step. Please note that I have modified and removed the co-ordinates of oxygen atoms from the pdb file. So, Its not exactly the standard format.
> My doubts are:
> 1. Am I wrong in thinking that in both the files, co-ordinates of same atoms in a particular time step should be same?
> 2. If I am wrong, then what is correct ?
> 3. If I am correct then  what may be the possible cause of having different coordinates in both the files?

The coordinates aren't different in terms of the numbers they actually 
represent.  Gromacs uses nm as a standard unit; PDB files use Angstrom.  Note 
that your numbers are different by exactly a factor of 10.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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